scholarly journals Triaging of Culture Conditions for the Enhanced Discovery of Secondary Metabolites from Different Bacteria

2020 ◽  
Author(s):  
Jenny Schwarz ◽  
Stephan Lütz
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Secondary Metabolite Production ◽  
Bacterial Strains ◽  
Metabolite Production ◽  
Desferrioxamine B ◽  
Prior Literature ◽  
Literature Coverage

Over the past decade, the One Strain Many Compounds (OSMAC) approach has been established for silent gene cluster activation and elicitation of secondary metabolite production, but so far the full secondary metabolome of a biosynthetically promising bacterium has not been elucidated yet. Here, we investigate the ability of seven categories of OSMAC conditions to elicit new mass features from bacterial strains with little literature coverage but high biosynthetic potential. The strains B. amyloliquefaciens DSM7, C. coralloides DSM2259, P. fallax HKI727, R. jostii DSM44719 and S. griseochromogenes DSM40499 were selected after genome mining with antiSMASH. After cultivation under OSMAC conditions, the generated extracts were subjected to LC/MS and MZmine analysis to determine new mass features, expressed gene clusters and evaluate the tested culture conditions. 4 predicted compounds, bacillibactin, desferrioxamine B, myxochelin A and surfactin, were identified and up to 147 new mass features were detected in the generated extracts, which greatly surpasses the number of predicted gene clusters. Among the new mass features are bioactive compounds which were so far unreported for the strains such as cyclo-(Tyr-Pro) from DSM7 and nocardamin from DSM2259. Furthermore, the tested culture conditions were evaluated regarding their suitability for the generation of new mass features from the selected strains and promising new starting points for further screenings are postulated. Especially culture conditions with little prior literature coverage are responsible for the activation of secondary metabolite production.

scholarly journals Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria

2020 ◽  
Author(s):  
Jenny Schwarz ◽  
Stephan Lütz
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Bacterial Strains ◽  
The Past ◽  
Desferrioxamine B ◽  
Prior Literature ◽  
The One ◽  
Literature Coverage

Over the past decade, the One Strain Many Compounds (OSMAC) approach has been established for silent gene cluster activation and elicitation of secondary metabolite production, but so far the full secondary metabolome of a biosynthetically promising bacterium has not been elucidated yet. Here, we investigate the ability of seven categories of OSMAC conditions to enhance the diversity of new mass features from bacterial strains with little literature coverage but high biosynthetic potential. The strains Bacillus. amyloliquefaciens DSM7, Corallococcus. coralloides DSM2259, Pyxidicoccus. fallax HKI727, Rhodococcus. jostii DSM44719, and Streptomyces. griseochromogenes DSM40499 were selected after genome mining with antiSMASH. After cultivation under OSMAC conditions, the generated extracts were subjected to LC-MS and MZmine analysis to determine new mass features and evaluate the tested culture conditions. 4 predicted compounds, bacillibactin, desferrioxamine B, myxochelin A, and surfactin, were identified and up to 147 new mass features were detected in the generated extracts, which greatly surpasses the number of predicted gene clusters. Among the new mass features are bioactive compounds that were so far unreported for the strains such as cyclo-(Tyr-Pro) from DSM7 and nocardamin from DSM2259. Furthermore, the tested culture conditions were evaluated regarding their suitability for the generation of new mass features from the selected strains and promising new starting points for further screenings are postulated. Especially culture conditions with little prior literature coverage are responsible for the activation of predicted gene clusters

scholarly journals Secondary Metabolite Production Potential of Mangrove-Derived Streptomyces olivaceus

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 332
Author(s):  
Dini Hu ◽  
Simon Ming-Yuen Lee ◽  
Kai Li ◽  
Kai Meng Mok
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Fermentation Broth ◽  
Genome Mining ◽  
Extreme Environments ◽  
Gene Clusters ◽  
Secondary Metabolite Production ◽  
Production Potential ◽  
Metabolite Production ◽  
Streptomyces Olivaceus

Mangroves are intertidal extreme environments with rich microbial communities. Actinobacteria are well known for producing antibiotics. The search for biosynthetic potential of Actinobacteria from mangrove environments could provide more possibilities for useful secondary metabolites. In this study, whole genome sequencing and MS/MS analysis were used to explore the secondary metabolite production potential of one actinobacterial strain of Streptomyces olivaceus sp., isolated from a mangrove in Macau, China. The results showed that a total of 105 gene clusters were found in the genome of S. olivaceus sp., and 53 known secondary metabolites, including bioactive compounds, peptides, and other products, were predicted by genome mining. There were 28 secondary metabolites classified as antibiotics, which were not previously known from S. olivaceus. ISP medium 2 was then used to ferment the S. olivaceus sp. to determine which predicted secondary metabolite could be truly produced. The chemical analysis revealed that ectoine, melanin, and the antibiotic of validamycin A could be observed in the fermentation broth. This was the first observation that these three compounds can be produced by a strain of S. olivaceus. Therefore, it can be concluded that Actinobacteria isolated from the mangrove environment have unknown potential to produce bioactive secondary metabolites.

scholarly journals Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 193
Author(s):  
Jenny Schwarz ◽  
Georg Hubmann ◽  
Katrin Rosenthal ◽  
Stephan Lütz
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Gene Clusters ◽  
Defined Medium ◽  
Culture Conditions ◽  
Aeration Rate ◽  
Culture Vessel ◽  
Desferrioxamine B ◽  
Rich Media ◽  
The One

Over the past decade, the one strain many compounds (OSMAC) approach has been established for the activation of biosynthetic gene clusters (BGCs), which mainly encode the enzymes of secondary metabolite (SM) biosynthesis pathways. These BGCs were successfully activated by altering various culture conditions, such as aeration rate, temperature, and nutrient composition. Here, we determined the biosynthetic potential of 43 bacteria using the genome mining tool antiSMASH. Based on the number of BGCs, biological safety, availability of deposited cultures, and literature coverage, we selected five promising candidates: Bacillus amyloliquefaciens DSM7, Corallococcus coralloides DSM2259, Pyxidicoccus fallax HKI727, Rhodococcus jostii DSM44719, and Streptomyces griseochromogenes DSM40499. The bacteria were cultivated under a broad range of OSMAC conditions (nutrient-rich media, minimal media, nutrient-limited media, addition of organic solvents, addition of biotic additives, and type of culture vessel) to fully assess the biosynthetic potential. In particular, we investigated so far scarcely applied OSMAC conditions to enhance the diversity of SMs. We detected the four predicted compounds bacillibactin, desferrioxamine B, myxochelin A, and surfactin. In total, 590 novel mass features were detected in a broad range of investigated OSMAC conditions, which outnumber the predicted gene clusters for all investigated bacteria by far. Interestingly, we detected mass features of the bioactive compounds cyclo-(Tyr-Pro) and nocardamin in extracts of DSM7 and DSM2259. Both compounds were so far not reported for these strains, indicating that our broad OSMAC screening approach was successful. Remarkably, the infrequently applied OSMAC conditions in defined medium with and without nutrient limitation were demonstrated to be very effective for BGC activation and for SM discovery.

scholarly journals Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 673
Author(s):  
Kattia Núñez-Montero ◽  
Damián Quezada-Solís ◽  
Zeinab G. Khalil ◽  
Robert J. Capon ◽  
Fernando D. Andreote ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Culture Media ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Bioactive Metabolites ◽  
Bacterial Strains ◽  
Antarctic Bacteria ◽  
New Antibiotics

Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new “-omics” comparative approaches for drug discovery.

scholarly journals Deletion of the Histone Deacetylase HdaA in Endophytic Fungus Penicillium chrysogenum Fes1701 Induces the Complex Response of Multiple Bioactive Secondary Metabolite Production and Relevant Gene Cluster Expression

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3657 ◽  
Author(s):  
Zhuang Ding ◽  
Haibo Zhou ◽  
Xiao Wang ◽  
Huiming Huang ◽  
Haotian Wang ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Secondary Metabolite ◽  
Endophytic Fungus ◽  
Penicillium Chrysogenum ◽  
Gene Clusters ◽  
Transcriptional Analysis ◽  
Secondary Metabolite Production ◽  
Metabolite Production ◽  
Epigenetic Regulator ◽  
Relevant Gene

Epigenetic regulation plays a critical role in controlling fungal secondary metabolism. Here, we report the pleiotropic effects of the epigenetic regulator HdaA (histone deacetylase) on secondary metabolite production and the associated biosynthetic gene clusters (BGCs) expression in the plant endophytic fungus Penicillium chrysogenum Fes1701. Deletion of the hdaA gene in strain Fes1701 induced a significant change of the secondary metabolite profile with the emergence of the bioactive indole alkaloid meleagrin. Simultaneously, more meleagrin/roquefortine-related compounds and less chrysogine were synthesized in the ΔhdaA strain. Transcriptional analysis of relevant gene clusters in ΔhdaA and wild strains indicated that disruption of hdaA had different effects on the expression levels of two BGCs: the meleagrin/roquefortine BGC was upregulated, while the chrysogine BGC was downregulated. Interestingly, transcriptional analysis demonstrated that different functional genes in the same BGC had different responses to the disruption of hdaA. Thereinto, the roqO gene, which encodes a key catalyzing enzyme in meleagrin biosynthesis, showed the highest upregulation in the ΔhdaA strain (84.8-fold). To our knowledge, this is the first report of the upregulation of HdaA inactivation on meleagrin/roquefortine alkaloid production in the endophytic fungus P. chrysogenum. Our results suggest that genetic manipulation based on the epigenetic regulator HdaA is an important strategy for regulating the productions of secondary metabolites and expanding bioactive natural product resources in endophytic fungi.

scholarly journals Secondary Metabolite Production by the Basidiomycete, Lentinus strigellus, under Different Culture Conditions

2012 ◽  
Vol 7 (6) ◽  
pp. 1934578X1200700 ◽  
Author(s):  
Bartholomeu A. Barros-Filho ◽  
Maria C. F. de Oliveira ◽  
Jair Mafezoli ◽  
Francisco G. Barbosa ◽  
Edson Rodrigues-Filho
Keyword(s):  
Secondary Metabolites ◽  
Liquid Medium ◽  
Secondary Metabolite ◽  
Culture Media ◽  
Indole Alkaloid ◽  
Culture Conditions ◽  
Secondary Metabolite Production ◽  
Metabolite Production ◽  
Czapek Medium

The basidiomycete Lentinus strigellus was cultivated in three different culture media and the secondary metabolites produced under different culture conditions were isolated and identified. When cultivated in a liquid medium with peptone, L. strigellus afforded the benzopyrans, 2,2-dimethyl-6-methoxychroman-4-one, 4-hydroxy-2,2-dimethyl-6-methoxychromane and (3 R,4 S)-3,4-dihydroxy-2,2-dimethyl-6-methoxychromane. The indole alkaloid echinuline and the anthraquinone fiscione, both unprecedented for the genus Lentinus, were isolated from the mycelium of the fungus. When cultured in Czapek medium enriched with potato broth, the fungus afforded the same benzopyrans except (3 S,4 S)-3,4-dihydroxy-2,2-dimethyl-6-methoxychromane. Panepoxydone and isopanepoxydone were also isolated when the microorganism was grown in Czapek medium.

scholarly journals Comparative genomics uncovers genetic diversity and synthetic biology of secondary metabolite production of the genus Trametes

2019 ◽  
Author(s):  
Yan Zhang ◽  
Jie Cao ◽  
Jingjing Wang ◽  
Yajun Cheng ◽  
Minghui Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Synthetic Biology ◽  
Secondary Metabolite ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Secondary Metabolite Production ◽  
Crystalline Cellulose ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Metabolite Production

Abstract It’s well-established that the CAZyme genes of genus Trametes contributed to the degradation processes of polysaccharides, including lignin or crystalline cellulose. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters of Trametes genus remain unclear. We conducted comparative analysis, detected the CAZyme genes, and predicted the biosynthetic gene clusters for 9 Trametes strains. Among 82,053 homologous clusters we obtained for genus Trametes, we identified 8,518 core genes, 60,441 accessory genes and 13,094 specific genes. Our results showed that a large proportion of CAZyme genes were catalogued into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes genus were divided into 6 strategies and the 9 Trametes strains harbored 47.78 BGCs on average. Our study uncovers the genus Trametes exhibited an open pan-genome structure, provides insights into the genetic diversity and explores the synthetic biology of secondary metabolite production for Trametes genus.

scholarly journals Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Ulysses Amancio de Frias ◽  
Greicy Kelly Bonifacio Pereira ◽  
María-Eugenia Guazzaroni ◽  
Rafael Silva-Rocha
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Gene Clusters ◽  
Secondary Metabolite Production ◽  
Special Focus ◽  
Biosynthetic Gene ◽  
Expression Systems ◽  
Biosynthetic Gene Clusters ◽  
Metabolite Production ◽  
Synthetic Promoters

Bacteria are a source of a large number of secondary metabolites with several biomedical and biotechnological applications. In recent years, there has been tremendous progress in the development of novel synthetic biology approaches both to increase the production rate of secondary metabolites of interest in native producers and to mine and reconstruct novel biosynthetic gene clusters in heterologous hosts. Here, we present the recent advances toward the engineering of novel microbial biosensors to detect the synthesis of secondary metabolites in bacteria and in the development of synthetic promoters and expression systems aiming at the construction of microbial cell factories for the production of these compounds. We place special focus on the potential of Gram-negative bacteria as a source of biosynthetic gene clusters and hosts for pathway assembly, on the construction and characterization of novel promoters for native hosts, and on the use of computer-aided design of novel pathways and expression systems for secondary metabolite production. Finally, we discuss some of the potentials and limitations of the approaches that are currently being developed and we highlight new directions that could be addressed in the field.

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